Variant report

Variant	rs2667783
Chromosome Location	chr15:77862529-77862530
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:77862030..77863568-chr15:77895689..77897664,2	MCF-7	breast:
2	chr15:77856989..77859495-chr15:77861940..77865382,3	K562	blood:
3	chr15:77861495..77863569-chr15:77924016..77925973,2	K562	blood:

Variant related genes	Relation type
ENSG00000169783	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1055691	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11635226	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11635634	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11636231	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12902072	0.81[EUR][1000 genomes]
rs12902898	0.81[EUR][1000 genomes]
rs12902948	0.81[EUR][1000 genomes]
rs12904200	0.81[EUR][1000 genomes]
rs12904208	0.81[EUR][1000 genomes]
rs12904533	0.81[EUR][1000 genomes]
rs12905044	0.81[EUR][1000 genomes]
rs12905318	0.81[EUR][1000 genomes]
rs12913005	1.00[CEU][hapmap];0.81[YRI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12914932	0.81[CEU][hapmap]
rs12915057	0.80[EUR][1000 genomes]
rs12917044	0.81[EUR][1000 genomes]
rs12917431	0.81[EUR][1000 genomes]
rs2516302	0.80[AMR][1000 genomes]
rs2667764	0.83[AMR][1000 genomes]
rs2667767	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2667775	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2667781	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2667782	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2682910	0.83[AMR][1000 genomes]
rs2682921	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2682922	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2682924	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2682927	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34075648	0.80[EUR][1000 genomes]
rs34607443	0.80[EUR][1000 genomes]
rs35657172	0.80[EUR][1000 genomes]
rs55883527	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs867916	0.80[AMR][1000 genomes]
rs907383	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs938090	0.83[AMR][1000 genomes]
rs939488	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1040852	chr15:77160237-78137541	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv916323	chr15:77485765-78121259	Enhancers Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1043284	chr15:77740632-77884026	Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv570139	chr15:77762493-77865459	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	nsv833060	chr15:77816654-78035204	Weak transcription Bivalent Enhancer Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
6	esv1806097	chr15:77817889-78301377	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
7	nsv904415	chr15:77845959-77943935	Weak transcription Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv904416	chr15:77845959-77967416	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv904417	chr15:77851535-77935992	Weak transcription Flanking Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv904418	chr15:77851535-77963887	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2667783	STRA6	cis	cerebellum	SCAN

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:77855600-77862600	Enhancers	Brain Cingulate Gyrus	brain
2	chr15:77857200-77862600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr15:77859400-77862600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr15:77860000-77862600	Enhancers	Fetal Stomach	stomach
5	chr15:77860000-77862800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr15:77860800-77862600	Enhancers	ES-I3 Cell Line	embryonic stem cell
7	chr15:77860800-77862600	Enhancers	HUES48 Cell Line	embryonic stem cell
8	chr15:77860800-77862600	Enhancers	HUES6 Cell Line	embryonic stem cell
9	chr15:77860800-77862800	Enhancers	Fetal Muscle Leg	muscle
10	chr15:77861000-77862600	Enhancers	Fetal Kidney	kidney
11	chr15:77861800-77862600	Enhancers	Fetal Lung	lung
12	chr15:77861800-77862800	Enhancers	Fetal Muscle Trunk	muscle
13	chr15:77862000-77862600	Enhancers	Fetal Heart	heart
14	chr15:77862000-77862600	Flanking Active TSS	HepG2	liver
15	chr15:77862000-77862800	Enhancers	Fetal Intestine Small	intestine
16	chr15:77862000-77869400	Weak transcription	Brain Anterior Caudate	brain
17	chr15:77862200-77862600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr15:77862200-77862600	Enhancers	Liver	Liver
19	chr15:77862200-77862600	Enhancers	K562	blood
20	chr15:77862200-77862800	Enhancers	Placenta	Placenta
21	chr15:77862200-77868200	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr15:77862200-77869000	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr15:77862200-77875000	Weak transcription	Left Ventricle	heart
24	chr15:77862400-77862600	Weak transcription	Fetal Brain Female	brain
25	chr15:77862400-77862600	Enhancers	Right Atrium	heart
26	chr15:77862400-77862800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr15:77862400-77862800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr15:77862400-77862800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr15:77862400-77863000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr15:77862400-77863600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr15:77862400-77863600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr15:77862400-77864800	Weak transcription	Brain Hippocampus Middle	brain
33	chr15:77862400-77865800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr15:77862400-77866600	Weak transcription	Lung	lung
35	chr15:77862400-77867200	Weak transcription	Stomach Mucosa	stomach
36	chr15:77862400-77868000	Weak transcription	Duodenum Mucosa	Duodenum
37	chr15:77862400-77868800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr15:77862400-77869400	Weak transcription	Brain Angular Gyrus	brain
39	chr15:77862400-77869400	Weak transcription	Brain Substantia Nigra	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links